Rosetta numbers residues from 1 and thus residue numbers in all input files have to be consistent with the fasta-sequence used for fragment picking and simulation. Often NMR targets have flexible tails and the flexibility can be predicted using TALOS+ or TALOS-N and the chemical shift information. We often trim such flexible termini which can help with convergence. To aid with trimming and inconsistent indices in files we provide the following applications
The trimming can be given by cmdline options -s and -e for start and end, respectively. In this case the numbering is relative to the input file. Alternatively, the trimming can be comfortably specified by providing the target fasta-sequence -fasta.